Do not fear princess; I will protect you. I will stand by your side through this battle. It is ours to win together.

These two have gone through some major shit

So my story for these two starts somewhere between 2-5 years after the current season of MLP. The mane six, while still very close friends, have each made personal strives in their lives. Rainbow dash trains wonderbolt cadets with Soarin, Applejack now owns the family farm, and many others are either married or in serious relationships, a couple even have children. So when its announced to a panic stricken twilight that Sombra has returned once again, it'd simply be cruel to pull her friends out of their lives to risk everything once again. Twilight, accompanied by Princess Luna, travel to the outskirts of the Crystal Empire where Sombra threatens to destroy the empire as a whole.

What they didn't know was that this was different. He appeared stronger than before. While he is ultimately vanquished by Luna, it didn't stop him from cornering and almost killing Twilight. She is left humiliated and physically weak for months afterward.

It's not until some time later that it's revealed that Sombra was able to cast one last spell before his death....